files.nc <- list.files("./input", pattern = "NC", full.names = T)
files.list.nc <- as.list(files.nc)
anno.nc <- read.table("./input/anno_neg_control.txt.gz", header = T, sep = "\t", stringsAsFactors = F)
myobj.nc <- methRead(
location = files.list.nc, sample.id = as.list(anno.nc$names),
assembly = "hg19", pipeline = "bismarkCoverage", header = F, skip = 0,
dbtype = "tabix", treatment = c(0,1,0,1,0,1), dbdir = "./output/methylDB"
)## Taking input= as a system command ('gunzip -c ./input/NC_rep1.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.## compressing the file with bgzip...## making tabix index...## Taking input= as a system command ('gunzip -c ./input/NC_rep2.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.## compressing the file with bgzip...## making tabix index...## Taking input= as a system command ('gunzip -c ./input/NC_rep3.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.## compressing the file with bgzip...## making tabix index...## Taking input= as a system command ('gunzip -c ./input/NC_rep4.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.## compressing the file with bgzip...## making tabix index...## Taking input= as a system command ('gunzip -c ./input/NC_rep5.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.## compressing the file with bgzip...## making tabix index...## Taking input= as a system command ('gunzip -c ./input/NC_rep6.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.## compressing the file with bgzip...## making tabix index...## compressing the file with bgzip...
## making tabix index...## flatfile located at: /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylBase_734d13f4dd63.txt.bgzfiles.sim <- list.files("./input", pattern = "sim_r", full.names = T)
files.list.sim <- as.list(files.sim)
anno.sim <- read.table("./input/anno_sim_data.txt.gz", header = T, sep = "\t", stringsAsFactors = F)
myobj.sim <- methRead(
location = files.list.sim, sample.id = as.list(anno.sim$names),
assembly = "hg19", pipeline = "bismarkCoverage", header = F, skip = 0,
dbtype = "tabix", treatment = c(0,1,0,1,0,1), dbdir = "./output/methylDB"
)## Taking input= as a system command ('gunzip -c ./input/sim_rep1.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.## compressing the file with bgzip...## making tabix index...## Taking input= as a system command ('gunzip -c ./input/sim_rep2.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.## compressing the file with bgzip...## making tabix index...## Taking input= as a system command ('gunzip -c ./input/sim_rep3.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.## compressing the file with bgzip...## making tabix index...## Taking input= as a system command ('gunzip -c ./input/sim_rep4.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.## compressing the file with bgzip...## making tabix index...## Taking input= as a system command ('gunzip -c ./input/sim_rep5.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.## compressing the file with bgzip...## making tabix index...## Taking input= as a system command ('gunzip -c ./input/sim_rep6.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.## compressing the file with bgzip...## making tabix index...## compressing the file with bgzip...
## making tabix index...## flatfile located at: /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylBase_734d4fba7119.txt.bgz## checking wether tabix file already exists:## ./output/methylDB/NC_rep1_tiled.txt.bgz## tabix file is new.## continuing now ...## compressing the file with bgzip...## making tabix index...## checking wether tabix file already exists:## ./output/methylDB/NC_rep2_tiled.txt.bgz## tabix file is new.## continuing now ...## compressing the file with bgzip...## making tabix index...## checking wether tabix file already exists:## ./output/methylDB/NC_rep3_tiled.txt.bgz## tabix file is new.## continuing now ...## compressing the file with bgzip...## making tabix index...## checking wether tabix file already exists:## ./output/methylDB/NC_rep4_tiled.txt.bgz## tabix file is new.## continuing now ...## compressing the file with bgzip...## making tabix index...## checking wether tabix file already exists:## ./output/methylDB/NC_rep5_tiled.txt.bgz## tabix file is new.## continuing now ...## compressing the file with bgzip...## making tabix index...## checking wether tabix file already exists:## ./output/methylDB/NC_rep6_tiled.txt.bgz## tabix file is new.## continuing now ...## compressing the file with bgzip...## making tabix index...## compressing the file with bgzip...
## making tabix index...## flatfile located at: /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylBase_734d48bb96d8.txt.bgz## two groups detected:
## will calculate methylation difference as the difference of
## treatment (group: 1) - control (group: 0)## checking wether tabix file already exists:## /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylDiff_734d48bb96d8.txt.bgz## tabix file is new.## continuing now ...## compressing the file with bgzip...## making tabix index...## flatfile located at: /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylDiff_734d48bb96d8.txt.bgz.bgz## checking wether tabix file already exists:## ./output/methylDB/sim_rep1_tiled.txt.bgz## tabix file is new.## continuing now ...## compressing the file with bgzip...## making tabix index...## checking wether tabix file already exists:## ./output/methylDB/sim_rep2_tiled.txt.bgz## tabix file is new.## continuing now ...## compressing the file with bgzip...## making tabix index...## checking wether tabix file already exists:## ./output/methylDB/sim_rep3_tiled.txt.bgz## tabix file is new.## continuing now ...## compressing the file with bgzip...## making tabix index...## checking wether tabix file already exists:## ./output/methylDB/sim_rep4_tiled.txt.bgz## tabix file is new.## continuing now ...## compressing the file with bgzip...## making tabix index...## checking wether tabix file already exists:## ./output/methylDB/sim_rep5_tiled.txt.bgz## tabix file is new.## continuing now ...## compressing the file with bgzip...## making tabix index...## checking wether tabix file already exists:## ./output/methylDB/sim_rep6_tiled.txt.bgz## tabix file is new.## continuing now ...## compressing the file with bgzip...## making tabix index...## compressing the file with bgzip...
## making tabix index...## flatfile located at: /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylBase_734d50e7e64d.txt.bgz## two groups detected:
## will calculate methylation difference as the difference of
## treatment (group: 1) - control (group: 0)## checking wether tabix file already exists:## /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylDiff_734d50e7e64d.txt.bgz## tabix file is new.## continuing now ...## compressing the file with bgzip...## making tabix index...## flatfile located at: /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylDiff_734d50e7e64d.txt.bgz.bgzc1 <- dmr.nc$qvalue[dmr.nc$qvalue <= 0.05]
datatable(
dmr.nc,
rownames = F,
filter = "top", extensions = c("Buttons", "ColReorder"), options = list(
pageLength = 10,
buttons = c("copy", "csv", "excel", "pdf", "print"),
colReorder = list(realtime = FALSE),
dom = "fltBip"
)
) %>%
formatStyle(
"qvalue",
backgroundColor = styleEqual(c1, rep("#66C2A5", length(c1)))
)## Warning in instance$preRenderHook(instance): It seems your data is too
## big for client-side DataTables. You may consider server-side processing:
## https://rstudio.github.io/DT/server.htmlc2 <- dmr.sim$qvalue[dmr.sim$qvalue <= 0.05]
datatable(
dmr.sim,
rownames = F,
filter = "top", extensions = c("Buttons", "ColReorder"), options = list(
pageLength = 10,
buttons = c("copy", "csv", "excel", "pdf", "print"),
colReorder = list(realtime = FALSE),
dom = "fltBip"
)
) %>%
formatStyle(
"qvalue",
backgroundColor = styleEqual(c2, rep("#66C2A5", length(c2)))
)## Warning in instance$preRenderHook(instance): It seems your data is too
## big for client-side DataTables. You may consider server-side processing:
## https://rstudio.github.io/DT/server.html## ─ Session info ──────────────────────────────────────────────────────────
## setting value
## version R version 3.5.1 (2018-07-02)
## os Ubuntu 16.04.5 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/Zurich
## date 2018-12-19
##
## ─ Packages ──────────────────────────────────────────────────────────────
## package * version date lib source
## assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.5.1)
## backports 1.1.3 2018-12-14 [1] CRAN (R 3.5.1)
## bbmle 1.0.20 2017-10-30 [1] CRAN (R 3.5.1)
## bindr 0.1.1 2018-03-13 [1] CRAN (R 3.5.1)
## bindrcpp 0.2.2 2018-03-29 [1] CRAN (R 3.5.1)
## Biobase 2.40.0 2018-10-04 [1] Bioconductor
## BiocGenerics * 0.26.0 2018-10-04 [1] Bioconductor
## BiocParallel 1.14.2 2018-07-08 [1] Bioconductor
## Biostrings 2.48.0 2018-10-29 [1] Bioconductor
## bitops 1.0-6 2013-08-17 [1] CRAN (R 3.5.1)
## callr 3.1.0 2018-12-10 [1] CRAN (R 3.5.1)
## cli 1.0.1 2018-09-25 [1] CRAN (R 3.5.1)
## coda 0.19-2 2018-10-08 [1] CRAN (R 3.5.1)
## colorspace 1.3-2 2016-12-14 [1] CRAN (R 3.5.1)
## crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.1)
## crosstalk 1.0.0 2016-12-21 [1] CRAN (R 3.5.1)
## data.table * 1.11.8 2018-09-30 [1] CRAN (R 3.5.1)
## DelayedArray 0.6.6 2018-09-11 [1] Bioconductor
## desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.1)
## devtools 2.0.1 2018-10-26 [1] CRAN (R 3.5.1)
## digest 0.6.18 2018-10-10 [1] CRAN (R 3.5.1)
## dplyr 0.7.8 2018-11-10 [1] CRAN (R 3.5.1)
## DT * 0.5 2018-11-05 [1] CRAN (R 3.5.1)
## emdbook 1.3.10 2018-05-19 [1] CRAN (R 3.5.1)
## evaluate 0.12 2018-10-09 [1] CRAN (R 3.5.1)
## fastseg 1.26.0 2018-10-04 [1] Bioconductor
## fs 1.2.6 2018-08-23 [1] CRAN (R 3.5.1)
## GenomeInfoDb * 1.16.0 2018-10-04 [1] Bioconductor
## GenomeInfoDbData 1.1.0 2018-10-04 [1] Bioconductor
## GenomicAlignments 1.16.0 2018-10-04 [1] Bioconductor
## GenomicRanges * 1.32.7 2018-09-20 [1] Bioconductor
## ggplot2 3.1.0 2018-10-25 [1] CRAN (R 3.5.1)
## glue 1.3.0 2018-07-17 [1] CRAN (R 3.5.1)
## gtable 0.2.0 2016-02-26 [1] CRAN (R 3.5.1)
## gtools 3.8.1 2018-06-26 [1] CRAN (R 3.5.1)
## htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.5.1)
## htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.5.1)
## httpuv 1.4.5 2018-07-19 [1] CRAN (R 3.5.1)
## IRanges * 2.14.12 2018-09-20 [1] Bioconductor
## jsonlite 1.6 2018-12-07 [1] CRAN (R 3.5.1)
## knitr 1.21 2018-12-10 [1] CRAN (R 3.5.1)
## later 0.7.5 2018-09-18 [1] CRAN (R 3.5.1)
## lattice 0.20-38 2018-11-04 [1] CRAN (R 3.5.1)
## lazyeval 0.2.1 2017-10-29 [1] CRAN (R 3.5.1)
## limma 3.36.5 2018-09-20 [1] Bioconductor
## magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.1)
## MASS 7.3-51.1 2018-11-01 [1] CRAN (R 3.5.1)
## Matrix 1.2-15 2018-11-01 [1] CRAN (R 3.5.1)
## matrixStats 0.54.0 2018-07-23 [1] CRAN (R 3.5.1)
## mclust 5.4.2 2018-11-17 [1] CRAN (R 3.5.1)
## memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.1)
## methylKit * 1.6.3 2018-10-12 [1] Bioconductor
## mime 0.6 2018-10-05 [1] CRAN (R 3.5.1)
## munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.1)
## numDeriv 2016.8-1 2016-08-27 [1] CRAN (R 3.5.1)
## pillar 1.3.1 2018-12-15 [1] CRAN (R 3.5.1)
## pkgbuild 1.0.2 2018-10-16 [1] CRAN (R 3.5.1)
## pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.5.1)
## pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.5.1)
## plyr 1.8.4 2016-06-08 [1] CRAN (R 3.5.1)
## prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.1)
## processx 3.2.1 2018-12-05 [1] CRAN (R 3.5.1)
## promises 1.0.1 2018-04-13 [1] CRAN (R 3.5.1)
## ps 1.2.1 2018-11-06 [1] CRAN (R 3.5.1)
## purrr 0.2.5 2018-05-29 [1] CRAN (R 3.5.1)
## qvalue 2.12.0 2018-11-28 [1] Bioconductor
## R.methodsS3 1.7.1 2016-02-16 [1] CRAN (R 3.5.1)
## R.oo 1.22.0 2018-04-22 [1] CRAN (R 3.5.1)
## R.utils 2.7.0 2018-08-27 [1] CRAN (R 3.5.1)
## R6 2.3.0 2018-10-04 [1] CRAN (R 3.5.1)
## Rcpp 1.0.0 2018-11-07 [1] CRAN (R 3.5.1)
## RCurl 1.95-4.11 2018-07-15 [1] CRAN (R 3.5.1)
## remotes 2.0.2 2018-10-30 [1] CRAN (R 3.5.1)
## reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.5.1)
## rlang 0.3.0.1 2018-10-25 [1] CRAN (R 3.5.1)
## rmarkdown 1.11 2018-12-08 [1] CRAN (R 3.5.1)
## rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.1)
## Rsamtools 1.32.3 2018-08-22 [1] Bioconductor
## rtracklayer 1.40.6 2018-08-31 [1] Bioconductor
## S4Vectors * 0.18.3 2018-10-04 [1] Bioconductor
## scales 1.0.0 2018-08-09 [1] CRAN (R 3.5.1)
## sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.1)
## shiny 1.2.0 2018-11-02 [1] CRAN (R 3.5.1)
## stringi 1.2.4 2018-07-20 [1] CRAN (R 3.5.1)
## stringr 1.3.1 2018-05-10 [1] CRAN (R 3.5.1)
## SummarizedExperiment 1.10.1 2018-10-04 [1] Bioconductor
## testthat 2.0.1 2018-10-13 [1] CRAN (R 3.5.1)
## tibble 1.4.2 2018-01-22 [1] CRAN (R 3.5.1)
## tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.5.1)
## usethis 1.4.0 2018-08-14 [1] CRAN (R 3.5.1)
## withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.1)
## xfun 0.4 2018-10-23 [1] CRAN (R 3.5.1)
## XML 3.98-1.16 2018-08-19 [1] CRAN (R 3.5.1)
## xtable 1.8-3 2018-08-29 [1] CRAN (R 3.5.1)
## XVector 0.20.0 2018-10-04 [1] Bioconductor
## yaml 2.2.0 2018-07-25 [1] CRAN (R 3.5.1)
## zlibbioc 1.26.0 2018-10-04 [1] Bioconductor
##
## [1] /home/ubuntu/R/x86_64-pc-linux-gnu-library/3.5
## [2] /usr/local/lib/R/site-library
## [3] /usr/lib/R/site-library
## [4] /usr/lib/R/library